April 28, 2011

Comparing five methods of admixture estimation

In my comments on the Moorjani et al. (2011) I argued that admixture proportions presented in the paper are inaccurate, and gave my reasoning behind this claim. Moorjani et al. (2011) also present STRUCTURE 2.2 results.

Naturally, I wanted to see whether independent admixture estimates on some of the same populations had been estimated in the literature. This brought me to Pugach et al. (2011) which introduced a wavelet-based admixture estimation method called StepPCO. In that paper, the authors presented estimates of the extent and timing of admixture for some populations also included in Moorjani et al. (2011). They also compared with HAPMIX, a well-known method using a completely different methodology, and presented their comparative data in this table and in the body of their paper.

Hence, we now have 4 different estimates of admixture for some populations. To these, I decided to add supervised ADMIXTURE 1.1 results. I used CEU and YRI as "West Eurasian" and "Sub-Saharan" references so that I would be in accordance with these other methods.

(The ADMIXTURE results were obtained by merging the datasets in PLINK with the --geno 0.001 option, then pruning the combined set for LD with --indep-pairwise 50 5 0.3)

The following table summarizes the estimates.

Note that these are estimates of Sub-Saharan admixture assuming two parental populations; also, Moorjani et al. break up the Bedouin sample into the two distinct groups it is composed of, so I have taken a weighted average of the figures in their paper.

It is difficult to make meaningful statistical inferences on only a few comparison points, but I do observe that STRUCTURE 2.2 on 13,900 markers gives the higher estimates, followed by Moorjani et al.

The other three methods cannot be ordered, giving higher estimates in some populations and lower in others. They all give, however, lower estimates than both Moorjani et al. (2011) and STRUCTURE.

As I've explained in my earlier post, Moorjani et al. (2011) have higher estimates of admixture because they measure it by comparing populations' shift on the East Eurasian-African axis, ignoring the Asian-shift of North Europeans and adding it to the African-shift of southern Caucasoids. This leads them to conclude a few percentage points of African admixture in populations that have virtually none (such as Sardinians and North Italians, even Swiss French). For populations that do have noticeable African admixture (such as those on the table) their overestimates amount to a a few percentage points.

Three of the methods also provide an estimate of time since admixture:

There is no simple relationship between these times, but an obvious pattern is that the dates of Moorjani et al. are younger, perhaps less than 50% of the other two methods.

Conclusion

Clearly, the art of admixture estimation is still in its infancy, and different methods provide different results even with a simple 2-population model. I've argued how the results of one method can be harmonized with those of the others, but I don't have a ready explanation about the substantial age differences. Pugach et al. argue that their method is better than HAPMIX, but the differences between the two seem small compared to the differences of both methods to ROLLOFF (the method of Moorjani et al.'s paper).

The discrepancy is even more interesting if one takes into account the fact that HAPMIX and ROLLOFF were done by many of the same people. Hopefully, someone will be able to figure out the cause behind the discrepancy. A commenter in my earlier post suggested that ROLLOFF produces younger ages because its age estimation is tied to its inflated admixture proportions; this could be true, however, the discrepancy exists even in populations where the relative difference is small.

A speculative historical coda

Historical explanations about the circumstances of this admixture need to be made with some caution, due to the uncertainty about admixture times.

For example, a doubling of the Moorjani et al. age estimates would disentangle the Sub-Saharan element in Levantine Arabs from the Islamic epoch. A doubling of the admixture date for Jewish populations, as presented by Moorjani et al. would bring that admixture's age to the middle of the 2nd millennium BC, a period in which the Hebrews were said to be in Egypt, where potentially they may have collectively acquired a small African admixture.

Hopefully, with time and full genome sequencing, we will get a better idea of what these African signals in some West Eurasian populations represent.

11 comments:

"A doubling of the admixture date for Jewish populations, as presented by Moorjani et al. would bring that admixture's age to the middle of the 2nd millennium BC, a period in which the Hebrews were said to be in Egypt, where potentially they may have collectively acquired a small African admixture. "

Dienekes,Even if you think the story of the Exodus has some historical element, it seems obvious from archaeology in Israel that the vast majority of "Jews" were actually the descendants of Cananites...who also may have mixed with people coming from the North or elsewhere (see Israel Finkelstein's work, by no means a Biblical Minimalist)

"it seems obvious from archaeology in Israel that the vast majority of "Jews" were actually the descendants of Cananites"

Wich in a way matches the biblical claims.

At least if it comes to "Israelites".

The bible claims, the northern tribes (Kingdom of Israel) are no real "Jews" anymore, because they intermixed with the Cananites and copied their religion and lifestyle and that this would be the reason, why god would make the Assyrians and Babylonians to destroy the northern tribes.

The southern tribes (Kingdom of Juda)saw themselfs as the only one true "Jews", by bloodline and culture. Or so the biblical claim is at 500 BC already.

But then again, the southern tribes also attracted the wrath of god, for their bloodline and culture was pure, but their faith was hollow and facade only.

The bible claims, the northern tribes (Kingdom of Israel) are no real "Jews" anymore, because they intermixed with the Cananites and copied their religion and lifestyle and that this would be the reason, why god would make the Assyrians and Babylonians to destroy the northern tribes.

If we take the Bible seriously (I usually don't), Israelites' purity or impurity should be irrelevant, as according to the Bible the Hebrew/Jewish line only continued through Judahites coming to a dead end in Israelites following the Assyrian destruction of the "Northern Kingdom".

Well, I don't think so, it is not about Israelites, but about all. It is a myth the South was so pure. The whole story of purity was more a way to deal with the stream of refugees coming from the North to the South after Israel was completely invaded (not that the South was very independent either). Archaeologists have found plenty of evidence that in the South there was nothing of this purity, but for avoiding pork. There were until very late all kinds of figures from different gods and there were altars in every hill, the Jews evolved from the tribes there for many centuries and they probably got influx from North and South. What the priests from the South did was to compose a narrative whereby their power in Jerusalem was seen as "the only true thing" and the house of their king the only true descendant of David.Check Finkelstein's view, which is fairly standard already.

I understand a project is being carried out by the University of Tel Aviv where also DNA analysis on ancient bones will play a role. I hope for the sake of science the project is conducted in a "kosher" way. It could help us unveal quite some links.

Kepler, I was just referring to what is written in the Bible (note that I write "If we take the Bible seriously (I usually don't)" and "according to the Bible"), not to the true motives behind what is written in the Bible, in response to Fanty's Bible-based arguments. Also do note that I am an atheist.

And I already know Finkelstein's work and approve of much of it.

I understand a project is being carried out by the University of Tel Aviv where also DNA analysis on ancient bones will play a role. I hope for the sake of science the project is conducted in a "kosher" way. It could help us unveal quite some links.

Even if you think the story of the Exodus has some historical element, it seems obvious from archaeology in Israel that the vast majority of "Jews" were actually the descendants of Cananites...who also may have mixed with people coming from the North or elsewhere (see Israel Finkelstein's work, by no means a Biblical Minimalist)

It's not entirely clear to me that material culture can track the movement of populations.

Take American Jews for example. How different are they really in their material culture from non-Jewish Americans? Or, the same for any of the other ethnic groups that live in the US?

Or, take the inventory of peoples from the Ancient Near East. We literally know the names of hundreds of now forgotten peoples, but only a few imperial ones (say the Persians, the Greeks, the Assyrians, the Arabs and a few more) have a presence that can be readily identified by material culture.

I read that there are some Jews in Jemen and southern Arabia who claim themselfs the last survivors of the 10 northern tribes.

Of course, anyone can claim anything. After all the "Thule society" (occult Proto-Nazis) claimed the Germanic peoples as the last survivors of Atlantis.And the Franks claimed themselfs to be the last survivors of Troy...

Like the Ashkenazi who claim to be Levites. The Ashkenazi "Levites" are 50% R1a1 and believed to be descants of the kingdom of Kaszhar instead of "real" Jews.

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